In this program, we will enable direct DNA methylation profiling during real-time DNA sequencing, without bisulfite conversion. We will accomplish this by tailoring Pacific Biosciences'high throughput Single-Molecule Real-Time (SMRT) DNA sequencing technology for the detection of altered DNA polymerase kinetics due to the presence of 5-methylcytosine (5mC) in the DNA template. In addition, we will develop five-base SMRT sequencing, in which the 5th base indicates the presence of 5mC in the original sample. Our proposed technologies offer several advantages over current methylation profiling techniques. For example, direct methylation sequencing without bisulfite conversion and DNA amplification will reduce the time and effort required for sample preparation. In addition, long reads provided by SMRT sequencing (several kilobases) will enable methylation analysis in highly-repetitive genomic regions. Pacific Biosciences is uniquely positioned to develop this technology because of our existing infrastructure of SMRT sequencing instrumentation and polymerase engineering resources. This program will create several new jobs within the next fiscal quarter, and, if successful, has the potential to create hundreds of new jobs as Pacific Biosciences delivers the technology to the broader research community. PUBLIC HEALTH RELEVANCE: Epigenomics is emerging as an ever more important aspect in the biology of development and disease processes such as cancer. We are proposing to develop a technique for direct, single base-pair resolution methylation profiling during real-time DNA sequencing, without bisulfite conversion. The ability to directly determine genomic DNA methylation patterns will dramatically speed up and reduce the cost of projects aiming to illuminate its role in human health.